Systems and methods for analyses of biological samples

Abstract

Disclosed are methods, systems, and articles of manufacture for performing a process on biological samples. An analysis of biological samples in multiple regions of interest in a microfluidic device and a timeline correlated with the analysis may be identified. One or more region-of-interest types for the multiple regions of interest may be determined; and multiple characteristics may be determined for the biological samples based at least in part upon the one or more region-of-interest types. Associated data that respectively correspond to the multiple regions of interest in a user interface for at least a portion of the biological samples in the user interface based at least in part upon the multiple identifiers and the timeline. A count of the biological samples in a region of interest may be determined based at least in part upon a class or type of data using a convolutional neural network (CNN).

The invention claimed is: 
     
       1. A method for analyzing biological samples, comprising:
 identifying an analysis of biological samples in multiple regions of interest in a microfluidic device and a timeline correlated with the analysis, wherein the timeline comprises information that is temporally aligned with at least one of a workflow or a pipeline of the analysis of the biological samples; 
 determining one or more region-of-interest types for the multiple regions of interest, wherein the one or more region-of-interest types comprise a target-based type correlated with at least one biological sample of the biological samples or a structure-based type correlated with the microfluidic device; 
 determining multiple characteristics for the biological samples based at least in part upon the one or more region-of-interest types, wherein the multiple characteristics respectively correspond to an attribute, a property, or a quantifiable metric for the biological samples or the analyses; 
 arranging and rendering associated data from the analysis that respectively correspond to the multiple regions of interest in a user interface for at least a portion of the biological samples based at least in part upon the multiple characteristics and the timeline; and 
 generating a bioinformatics pipeline view, generating the bioinformatics pipeline view comprising:
 determining a sequencing dataset for the biological samples in a plurality of chambers or the multiple regions of interest of the microfluidic device, wherein a biological sample comprises a sequence of nucleotides or amino acids. 
 
 
     
     
       2. The method of  claim 1 , wherein arranging and rendering the associated data comprises:
 determining a gallery structure having a plurality of gallery sub-structures for the analysis results based at least in part upon an allocable space in the user interface for rendering the analysis results. 
 
     
     
       3. The method of  claim 2 , wherein arranging and rendering the analysis results comprises:
 populating the analysis results into the plurality of gallery sub-structures in a gallery structure based at least in part upon a characteristic of the multiple characteristics. 
 
     
     
       4. The method of  claim 3 , determining the gallery structure comprising:
 determining a first sequence of data correlated with a set of time points or time periods for a first biological sample obtained from a first region of interest of the multiple regions of interest from the gallery structure stored in an addressable space in a non-transitory computer accessible storage medium, wherein the first sequence of data corresponds to at least a first characteristic of the multiple characteristics; 
 determining a second sequence of data correlated with the set of time points or time periods for a second biological sample obtained from a second region of interest of the multiple regions of interest from the gallery structure, wherein the second sequence of data corresponds to at least a second characteristic of the multiple characteristics; and 
 in response to a selection of the at least the first characteristic from the multiple characteristics with a first selection widget in the user interface, extracting a first value of at least the first characteristic from a plurality of values for the first biological sample or for the analysis; and 
 extracting a second value of at least the first characteristic from the plurality of values for the second biological sample or for the analysis. 
 
     
     
       5. The method of  claim 4 , arranging and rendering analysis results comprising:
 rendering a first interactive object and a second interactive object respectively corresponding to the first sequence of data and the second sequence of data into the gallery view, wherein the first interactive object is representative of the first value for the first biological sample or for the analysis, and the second interactive object is representative of the second value for the second biological sample or for the analysis. 
 
     
     
       6. The method of  claim 1 , further comprising:
 in response to an invocation of a timeline view through a timeline view activation interactive widget in the user interface based at least in part upon the timeline, rendering the timeline view and a matching grid portion in the user interface. 
 
     
     
       7. The method of  claim 6 , wherein
 the timeline view comprises a respective progress of multiple workflow tasks in the analysis of the biological samples, and 
 the respective progress graphically indicates respective temporal durations of the multiple workflow tasks. 
 
     
     
       8. The method of  claim 1 , further comprising:
 associating a first region of interest of the multiple regions of interest with one or more graphical elements illustrated in a timeline view. 
 
     
     
       9. The method of  claim 8 , wherein arranging and rendering the analysis results comprises:
 determining the timeline based at least in part upon the pipeline or the workflow for the analysis of the biological samples. 
 
     
     
       10. The method of  claim 9 , wherein arranging and rendering the analysis results comprises:
 determining a plurality of stages for the analysis based at least in part upon the timeline, wherein the plurality of stages respectively corresponds to a plurality of timepoints or time periods for the analysis of the biological samples. 
 
     
     
       11. The method of  claim 10 , wherein rendering the respective analysis results comprises:
 respectively determining a plurality of graphic representations for the plurality of stages based at least in part upon the plurality of timepoints or time periods. 
 
     
     
       12. The method of  claim 1 , further comprising rendering a data control view in the user interface, rendering the data control view comprising:
 generating a microfluidic device data structure having a plurality of fields for the microfluidic device having a plurality of chambers. 
 
     
     
       13. The method of  claim 12 , rendering the data control view comprising:
 populating first data correlated with the microfluidic device into a first field in the microfluidic device data structure, wherein the first data comprises a first identifier of the microfluidic device. 
 
     
     
       14. The method of  claim 1 , further comprising rendering a filter view, wherein rendering the filter view comprises:
 determining a first filter type for a first filter based at least in part upon an execution of one or more instructions triggered by an interaction with a first filter selector switch in a filter generation module. 
 
     
     
       15. The method of  claim 14 , rendering the filter view further comprising:
 dynamically determining and displaying, in the filter view for the microfluidic device, a first total number of regions of interest for a first set of filtered regions of interest that satisfies a first dynamic constraint of the first filter applied to the multiple regions of interest. 
 
     
     
       16. The method of  claim 14 , rendering the filter view further comprising:
 generating, at a filter generation module, a logical combination of at least a second filter of a second filter type and the first filter of the first filter type. 
 
     
     
       17. The method of  claim 1 , generating the bioinformatics pipeline view further comprising:
 in response to a first interaction with a first sequencing view widget in the user interface, rendering a first sequencing view in the bioinformatics pipeline view that illustrates a distribution of an attribute of the sequence of first biological samples including at least one of a sequence of nucleotides, a sequence of amino acids, or a sequence of macromolecules in the plurality of chambers or the multiple regions of interest of the microfluidic device. 
 
     
     
       18. The method of  claim 17 , generating the bioinformatics pipeline view further comprising:
 overlaying the first sequencing view with first information that comprises one or more statistical measures of the distribution of the attribute of multiple sequences of first biological samples including the sequence of first biological samples, wherein the user interface comprises a total number of the multiple sequences of first biological samples, a total number of regions of interest having the sequence of first biological samples, and a respective total number of one or more sequences of first biological samples in a respective region of interest of the array of regions of interest. 
 
     
     
       19. The method of  claim 1 , wherein the multiple characteristics correspond to one or more attributes that further comprise at least one of an identifier of a region of interest in the microfluidic device, a size attribute of the biological samples, a maximum brightness attribute for the biological samples, a minimum brightness attribute for the biological samples, a first pixel count attribute in a first direction for a centroid of a first biological sample, a second pixel count attribute in a second direction for the centroid of the biological sample, a size attribute for the centroid of the biological sample, a time lapse index attribute, a device identifier for the microfluidic device, a biological sample count attribute, a verified biological sample count attribute, a biological sample type attribute, a score attribute of the plurality of regions of interest, a gate path index, an area pixel attribute, a background pixel attribute, or a median brightness attribute for the plurality of biological samples. 
     
     
       20. An article of manufacture comprising a non-transitory machine accessible storage medium storing thereupon a sequence of instructions which, when executed by a processor, causes the process to perform the method of  claim 1 . 
     
     
       21. A system, comprising:
 a processor; 
 a user interface coupled to the processor for processing a plurality of molecular-biological samples that comprise a first molecular-biological sample and a second molecular-biological sample in a first molecular-biological device; 
 a non-transitory computer accessible storage medium storing thereupon a sequence of instructions which, when executed by a processor, causes the processor to perform any of the method of  claim 1 .